'Cosmogony' is the study of the origin of the universe, is an area where science and theology meet. Creation was a supernatural event. That is, it took place outside of the natural realm. This fact introduces something which exists outside of the natural, the Spiritual realm. Bible just declares that God is the Creator of all things. It does not attempt to prove it. Nor it attempts to explain how He did the Creation. Here what God does not tell us is very important. God chose not to elaborate the complex engineering went into His creation. He did not tell us, for example, how He created the light or how the tiny neurons in our bodies function in the internal communication. Hence many have concluded that the creation account is contrary to proven scientific facts and cannot be reconciled with geologic and astronomical discoveries of the last few centuries. Even some who claim to believe the Bible's moral and ethical principles discount 'Genesis 1' as scientifically unreliable, relegating it to mere "Hebrew poetry"! Here we need to understand,
1. The creation account in Genesis is a very brief, condensed version of what actually happened when God created the heavens and the earth. God did not fill in the details.
2. Its focus is on how God prepared the earth for human habitation. The creation of other portions of the universe is treated as incidental to making the earth ready for mankind. 
However, following are the some of the objections of unbelievers of God's Creation, which I will try to deal with in this article.
1. If God created everything, than how God came into existence?
The question can be put in other words - If Universe has a cause, what is the cause of God?
We are in the physical realm, which is controlled by certain principles. Our entire universe is bound by time-dimension apart from others. Since God, by definition, is the creator of the whole universe, He is the creator of time. He being in Spiritual realm is not limited by the time dimension He created, so has no beginning in time. Therefore He doesn't have a cause. God, unlike the universe, had no beginning, so doesn't need a cause.  Einstein's Theory of Relativity demonstrates by experimental evidence that time is linked to matter and space. Einstein illustrated it in the following example: Consider two persons of same age. If one of them travels in space for few years at the speed of light and returns to earth, he will have less age than the person who is residing on the earth. This means the first person has travelled in time. However, travelling at such high speeds is technically not viable at present.
2. God is not the Creator. Origin of the Universe can be explained through science:
Many of the scientific discoveries changed the way we live. But we need to consider them as blessings of God, which calls for humility. Great scientists like Copernicus, Kepler, Galileo, Newton, Mendel, Thomson Kelvin, Michael Faraday, and Albert Einstein apart from their genius, acknowledge the divine hand in their outstanding discoveries. But sadly some skeptics take pride in their intellectual ability and like to think that they have no "beliefs."
I believe no major scientific genius design is comparable to the God's design of Creation in all its splendid. Just think of the simple act of seeing? Scientists tell us that the delicate engineering of the eye's cornea and lens make the most advanced camera seem like a child's toy by comparison. The tiny rods and cones in the eye change light into electro-chemical impulses through processes the most sophisticated laboratory can't reproduce. And brain cells transform these electrical impulses into the miracle of perception - something no high-tech computer can come close to doing. 
Often scientific theories fail to give satisfactory explanation of why a certain object in Nature behaves the way it does. David Mills puts it in his 'Atheist Universe': "If I ask why a rock thrown skyward soon falls back to Earth, it would be meaningless to respond, "It's the law of gravity." "Gravity" or "the law of gravity" is simply the name and description we assign to the observed phenomenon. The true, underlying reason why all objects in the universe attract each other is, to this day, a baffling enigma. True, Einstein showed that massive objects distort space-time and produce gravitational effects. But why do massive objects distort space-time? Such questions are still unanswered. A physical law, then, is a man-made description, rather than a causal explanation, of how the universe consistently behaves." Einstein, who is considered one of the great scientists in the field of light, while commenting on the complexity of nature of light, once said: "If anybody thinks that he knows what is light, he is fooling himself". Even today scientists are unable explain what is light. The famous Big Bang theory too has serious pit falls and tries to overlook the question of the origin of physical matter for the 'Big Bang'.
3. Show me God. God does not exist:
Millions believe God. Few have proof. Why God does not reveal Himself to all. The reason lies in the nature and plan of God. God is regularly intervening in human history in answer to His servant's prayers. But God's acts are so subtly designed, that the person who received the miracle knows it is done by God. But for the rest of the world it is a natural incidence.
Jesus illustrates it in Mat 13:10-13 (NIV). The disciples came to Him (Jesus) and asked, "Why do You speak to the people in parables?" He replied, "The knowledge of the secrets of the kingdom of heaven has been given to you, but not to them. Whoever has will be given more, and he will have an abundance. Whoever does not have, even what he has will be taken from him. This is why I speak to them in parables: "Though seeing, they do not see; though hearing, they do not hear or understand.
In His interventions, God normally uses the Nature to perform His supernatural works, making it further difficult to trace His dealings. Such mysterious works of God, for instance, we can observe when God intervened in Israel history while rescuing them from the slavery in Egypt. The plagues God sent on Egypt, as describe in Exodus, are common in Egyptian climates, such as plagues of locusts, hail, boils, gnats and plague on livestock etc. When each plague struck, King Pharaoh immediately recognized it as God's work. But after a while he was convinced that these would have been natural incidences. When God divided the Jordan River, it is a miracle for Israelites and is only a natural geographic phenomenon to the scientific community.
4. If God is the Creator of all things, why He allows evil or misery in His Creation?Although this question is not directly related to Creation, the issue has become a stumbling block for many in believing God as their Creator.
First let us deal with evil. Although God did not create or encourage evil in the world, God gave the human beings the free will. Thanks to God, He did not create us like robots, but gave us the free will to choose between good and bad or God and Mammon. Many of the evil in the world are caused by our own actions. Natural world follows its own laws. Take for example natural disasters. You know that a certain place is prone for earth quakes and still you live there because you like the place or for the livelihood. Finally you blame God when the disaster strikes. Things of the world normally follow their natural course according to natural laws. For instance, if a plane crashes, that could be due to a technical snag or a pilot error or even a terrorist act. The Christians and non-Christians in the plane are bound to meet the disaster equally. But of course, this is not the case always. Sometimes God does intervene and does step into action according to His will, especially when His ultimate plan (for instance salvation) is threatened or He is moved by a prayer or an intercession for protection. This is the great comfort for us as believers that God is in control and He is willing to listen to our prayers. All the scientific and natural laws will fail, once God steps into action.
Coming to the pain, Keith Miller once said, "Pain is like a fertilizer. It sinks when you're around it, and you hate it. But after a while you realize that that despicable stuff provided the nutrients for your growth". Everybody agrees pain and disappointment builds character and perseverance. However, Happiness and misery, psychologists say, are a matter of perception. That's why we can see some of the happier faces from the huts in a slum than the people living in palatial buildings.
If it is real unbearable physical pain or a situation beyond control, that's the time one will turn to their Creator, which again is for their ultimate good. Furthermore for the secular world, if a person dies everything is over. But that's not the case with the believers, as Jesus did for Lazarus.
About Author / Additional Info:
4 Mills David, Atheist Universe, Ulysses Press, 2006.